Contacts of the helix formed by residues 485 - 490 (chain J) in PDB entry 2FRV
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with PRO 485 (chain J).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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369J VAL* 3.5 13.3 - - + +
463J ARG* 3.2 30.7 - - + +
464J GLY* 3.5 23.1 - - - +
465J MET 3.5 17.4 - - - +
466J LEU* 4.0 3.1 - - + -
484J VAL* 1.3 93.6 - - + +
486J SER* 1.3 60.3 + - - +
488J TRP* 3.0 16.3 + - + +
489J ASN* 3.1 13.7 + - - -
537J FCO 3.2 35.0 - - - +
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Residues in contact with SER 486 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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357J MET* 3.6 7.3 - - - +
463J ARG* 4.3 3.0 + - - +
484J VAL 3.3 0.4 - - - -
485J PRO* 1.3 74.7 - - - +
487J THR* 1.3 57.4 + - - +
489J ASN* 4.5 4.8 + - - +
490J LEU* 3.0 42.7 + - - +
527J TYR 5.2 0.3 + - - -
528J ASP 4.0 3.6 + - - -
529J PRO* 3.9 4.7 - - - +
530J CYS* 3.1 41.9 + - - +
534J GLY* 4.2 4.7 - - - -
537J FCO 2.8 25.1 + - - -
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Residues in contact with THR 487 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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321J GLU* 4.1 9.9 - - - +
357J MET* 4.0 7.9 - - + -
358J LYS* 3.3 34.8 - - + +
360J PRO* 3.2 31.0 - - + +
361J ARG* 5.6 0.2 + - - -
484J VAL* 2.8 27.9 + - - +
486J SER* 1.3 77.1 - - - +
488J TRP* 1.3 61.8 + - - +
491J GLY* 3.3 17.7 + - - -
534J GLY* 2.8 31.0 + - - +
536J HIS* 4.0 5.0 - - + -
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Residues in contact with TRP 488 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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281J LEU* 4.4 11.2 - - + -
314J PHE* 6.3 0.2 - + - -
319J ILE* 4.1 28.7 - - + -
360J PRO* 3.5 43.3 - - + +
361J ARG* 3.9 22.8 + - - -
362J TYR* 3.7 27.8 - - + -
367J PHE* 3.9 40.3 + - + +
369J VAL* 3.6 25.0 - - + +
465J MET* 4.0 23.8 + - - -
483J VAL* 3.8 14.4 + - + +
484J VAL 3.3 23.4 + - - -
485J PRO* 3.0 9.8 + - + +
487J THR* 1.3 81.3 - - - +
489J ASN* 1.3 62.7 + - - +
491J GLY 4.1 2.4 + - - -
500J SER* 4.2 10.0 - - - -
501J ALA 4.4 1.2 + - - -
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Residues in contact with ASN 489 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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368J GLU* 3.6 12.3 - - - +
369J VAL* 3.2 42.1 + - - +
463J ARG* 3.8 10.3 + - - +
485J PRO 3.1 15.9 + - - +
486J SER* 4.5 3.0 + - - +
488J TRP* 1.3 75.0 - - - +
490J LEU* 1.3 67.7 + - + +
491J GLY 3.7 0.2 - - - -
500J SER* 3.7 1.0 + - - -
501J ALA* 3.6 10.2 + - - -
502J VAL* 2.9 31.0 + - - +
527J TYR* 3.6 35.0 + - + +
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Residues in contact with LEU 490 (chain J).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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21J LEU* 3.8 29.8 - - + -
23J ILE* 5.4 0.4 - - + -
37J SER* 2.8 31.9 + - - +
39J SER* 4.3 2.8 + - - +
355J SER* 5.0 0.2 + - - -
357J MET* 3.8 19.3 - - + +
486J SER* 3.0 26.3 + - - +
489J ASN* 1.3 85.7 - - + +
491J GLY* 1.3 63.0 + - - +
492J PRO* 4.7 0.2 - - - +
500J SER* 4.3 0.2 - - - -
502J VAL* 3.9 24.0 - - + -
524J VAL* 4.8 0.4 - - + -
527J TYR* 4.6 7.9 - - + +
529J PRO* 3.3 42.0 - - + -
530J CYS 4.6 0.2 - - - +
531J ILE* 4.5 2.2 - - + -
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il